Medical procedures such as endoscopy (e.g., bronchoscopy) may involve the insertion of a medical tool into a patient's luminal network (e.g., airways) for diagnostic and/or therapeutic purposes. In certain procedures, one or more of robotic arm(s) are aligned with the patient prior to initiating the procedure. Alignment of the robotic arm(s) provides the system with positional information which relates the position of the robotic arm(s) to the patient. The robotic arm(s) may be manually repositioned by a user of the system during alignment of the robotic arm(s) with the patient.